Algal biotechnology has strong potential to solve pressing challenges relating to the availability of food, renewable energy and climate change. Yet the tools for algal biotechnology do not currently allow for swift adoption of the organisms for synthetic biology applications. Main areas of research that need attention are: high level transgene expression, targeted integration, homologous recombination, elimination of silencing, ability to efficiently deliver large sections of heterologous DNA as well as robust tools for production organisms. Methods and compositions delineated below seek to address these challenges thru commercialization of advanced synthetic biology toolkits for algal hosts.